Read on Twitter
1/23 WHY WE ARE BUILDING AN OPEN PLAYBOOK FOR DEPLOYING GENOMIC PATHOGEN SURVEILLANCE.
Primarily for developing countries, but smaller towns in developed countries would also find this useful.
Primarily for developing countries, but smaller towns in developed countries would also find this useful.
2/ I cover the WHY and WHY NOW of genomic pathogen surveillance in this other thread. https://twitter.com/kcorazo/status/1258698778606858240
3/ In this thread, I'd like to focus why the need now is scaling deployment—PROJECT MANAGEMENT:
Enabling technology has matured a lot: @nanopore
Scientists have repeatedly shown its feasibility https://scrapbox.io/kahlil/lab-in-suitcase_papers
Deployment playbook
Enabling technology has matured a lot: @nanopore Scientists have repeatedly shown its feasibility https://scrapbox.io/kahlil/lab-in-suitcase_papersDeployment playbook
4/ Let me do a quick review of the state of technology innovation, and lab-in-suitcase papers, then I'll show what a deployment playbook looks like.
5/ It seems the biggest **technology** challenge right now are reagents: prices, logistics and stability in tropical climates.
I wonder if projects like this will eventually fix this issue: https://app.jogl.io/project/174/ @Eyesgack https://twitter.com/arwynedwards/status/1259101958813691909
I wonder if projects like this will eventually fix this issue: https://app.jogl.io/project/174/ @Eyesgack https://twitter.com/arwynedwards/status/1259101958813691909
6/ Other innovations continue to lower costs. For instance, multiplexing, which allows multiple samples to be sequenced in a run, is increasing in capacity, thus lowering cost per sample https://nanoporetech.com/resource-centre/nanopore-sequencing-sars-cov-2-genome-introduction-protocol
7/ In the software side, "adaptive sampling". The sequencer can release the nucleic acid being read, based on real-time comparison w reference genomes. Flowcells are expensive, and this would increase their capacity by lessening reads of unwanted sections. https://twitter.com/mattloose/status/1224350276083240960
8/ @kirstynbrunker et al recently updated their paper. https://wellcomeopenresearch.org/articles/5-3 With "nuclease-flush", which allows multiple runs per flowcell, they estimate the cost per sample to drop to ~£35 to £45. https://twitter.com/kcorazo/status/1258698830666543105
9/ [[ @laura_boykin]] et al estimate that with the Flongle, cost could go down to as low as 4 USD https://www.mdpi.com/2073-4425/10/9/632/htm
![9/ [[ @laura_boykin]] et al estimate that with the Flongle, cost could go down to as low as 4 USD https://www.mdpi.com/2073-4425/10/9/632/htm](https://pbs.twimg.com/media/EZLfpndUEAAaRrz.png "9/ [[ @laura_boykin]] et al estimate that with the Flongle, cost could go down to as low as 4 USD https://www.mdpi.com/2073-4425/10/9/632/htm")
10/ [[ @waywardsyintist]] - who used nanopore to for arbovirus genomic surveillance in the field https://www.nature.com/articles/s41598-018-23641-7 - has started a company to provide a lab-in-suitcase solution based on that experience. My guess is that there will be more to come. https://twitter.com/waywardsyintist/status/1251238460796612608
11/ [[Ahmed Abd El Wahed]]'s suitcase lab is EUR8,000 excluding the laptop https://nanoporetech.com/resource-centre/nanopore-sequencing-missing-puzzle-piece-molecular-identification https://twitter.com/kcorazo/status/1258698836584759298
12/ This list from [[ @NetworkArtic]] for sequencing Ebola gives us an idea
Reagents: £6,890
Equipment: £6,890
Consumables: £887
Cold Chain, Power, Storage: £2,686
Grand total: **£17353**
https://artic.network/ebov/ebov-seq-kit.html
Reagents: £6,890Equipment: £6,890Consumables: £887Cold Chain, Power, Storage: £2,686Grand total: **£17353**https://artic.network/ebov/ebov-seq-kit.html
13/ The tech is ready and it is affordable. Scientists have shown feasibility. But how come developing countries are very slow in producing SARS-CoV-2 genomes? https://twitter.com/laura_boykin/status/1264922619813351424
14/ The article linked to by [[ @laura_boykin]] above gives some answers.
They have the equipment and training.
But there is lack of collaboration (eg, sampling org to sequencing org).
Gov't employee mindset: needs top-down orders to change work direction
They have the equipment and training. But there is lack of collaboration (eg, sampling org to sequencing org).Gov't employee mindset: needs top-down orders to change work direction
15/ cont.
Lack of funding from govt (I suppose this is for reagents and other consumables considering they have equipment and training)
(prior to reading this, I assumed the biggest problems were lack of trained personnel and logistics of bringing in reagents)
Lack of funding from govt (I suppose this is for reagents and other consumables considering they have equipment and training)(prior to reading this, I assumed the biggest problems were lack of trained personnel and logistics of bringing in reagents)
16/ These sound to me like project management problems.
Aligning work to what's needed to accomplish the project
Working through the politics of organizations
Ultimately, being the single point of responsibility for getting the project done, on-time, on-scope and on-budget
Aligning work to what's needed to accomplish the projectWorking through the politics of organizationsUltimately, being the single point of responsibility for getting the project done, on-time, on-scope and on-budget
17/ Given new low-cost alternatives to sequencing, why even work with large bureaucracies? What's stopping university labs, private labs and local government units from doing the sequencing themselves? Am I naive to think that this is simply a matter of execution?
18/ What does execution—the deployment of genomic pathogen surveillance—actually mean? There's actually an answer to that, just like there's an answer to "what's the right way to do accounting?" GAAP for the latter; PMBOK for the former https://en.wikipedia.org/wiki/Project_Management_Body_of_Knowledge
19/ So how would a project management playbook for deploying genomic surveillance look like? Here's what a professional project manager would look for or create. https://scrapbox.io/kahlil/Resources:_Open_Playbook_for_Deploying_Genomic_Surveillance
20/ A deployment in one location would be very similar to another one, so why not reuse these project planning and execution tools? Just include some project management training for first-time PMs.
This is essentially our JOGL project https://app.jogl.io/project/285
This is essentially our JOGL project https://app.jogl.io/project/285
21/ To get an idea of what these project management tools are, please check this other thread https://twitter.com/kcorazo/status/1266227623958507520
22/ The urgent need is to provide richer SARS-CoV2 data for each locality. But it goes beyond COVID. According to the WHO, rabies kills 59,000 people/yr. In this map of arboviruses (eg, Dengue, Zika), we see that the worst hit is the developing world. https://www.sciencedirect.com/science/article/pii/S1201971217303089
23/23 Most of the work is PM, which me and @akinnaija could handle. However, subject matter experts in lib prep and bioinformatics would be helpful: just be in our Slack channel to see that we are not doing anything stupid & to answer occasional technical questions. Pls DM me!
